The FGA package for GAP provides methods for computations with finitely generated subgroups of free groups.
It allows you to (constructively) test membership and conjugacy, and to compute free generators, the rank, the index, normalizers, centralizers, and intersections where the groups involved are finitely generated subgroups of free groups.
In addition, it provides generators and a finite presentation for the automorphism group of a finitely generated free group and allows to write any such automorphism as word in these generators.